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library(dplyr)

##### HIGH FAT DIET RAT  #47 SAMPLES, 4 SIG GENES
hf_nor_2PCR

##### HIGH FAT DIET RAT #23 SAMPLES
high_fat

##### NORMAL DIET RAT # 24 SAMPLES
normal_diet

#####HUMAN # 24 SAMPLES - ALL GENES
hpcr_nor

#####RAT #  48 SAMPLES - ALL GENES - HIGH FAT & NORMAL DIET - FOLD CHANGE NON NORM
hf_2PCR

############################
### AUTOMATIC
fx_z <- function(gene) {
  gene_std <- (gene - (mean(gene))/(sd(gene)))
  return(gene_std)
}
############################
####MANUAL INPUT
fx_z2 <- function(gene,mean,sd) {
  gene_std <- (gene - (mean)/(sd))
  return(gene_std)
}
############################
#mean(hf_2PCR$CERKL)
#sd(hf_2PCR$CERKL)
############################
#mean(hf_2PCR$FA2H)
#sd(hf_2PCR$FA2H)
#############################
shapiro.test(fx_z(hf_2PCR$CERKL))

    Shapiro-Wilk normality test

data:  fx_z(hf_2PCR$CERKL)
W = 0.90197, p-value = 0.000833

shapiro.test(fx_z(hf_2PCR$FA2H))

    Shapiro-Wilk normality test

data:  fx_z(hf_2PCR$FA2H)
W = 0.98597, p-value = 0.838

#hf_nor_2PCR = ALL RAT // NON NORMALIZED
library(dplyr)
ALLRAT <- select(hf_nor_2PCR, -SPECIES, -CHRNA10, -SMYD1)
NUM <- ALLRAT[,4:5]
AR_1 <- fx_z(NUM$CERKL)
AR_2 <- fx_z(NUM$FA2H)
LAB <- ALLRAT[,1:3]
ALLRAT_2 <- data.frame(LAB,AR_1,AR_2)
#hf_2PCR
NORMALDIET <- ALLRAT_2[1:24,2:5]
HF_DIET <- ALLRAT_2[25:47,2:5]
shapiro.test(AR_2)

    Shapiro-Wilk normality test

data:  AR_2
W = 0.96974, p-value = 0.2589

shapiro.test(AR_1)

    Shapiro-Wilk normality test

data:  AR_1
W = 0.94885, p-value = 0.03903

names(ALLRAT_2)[4] <- 'CERKL'
names(ALLRAT_2)[5] <- 'FA2H'
names(NORMALDIET)[4] <- 'FA2H'
names(NORMALDIET)[3] <- 'CERKL'
names(HF_DIET)[4] <- 'FA2H'
names(HF_DIET)[3] <- 'CERKL'
hf_2PCR

NORMAL <- ALLRAT_2[1:24,]
HIGH_FAT <- ALLRAT_2[24:47,]
ALLRAT_2

ALLRAT_2

NORMALDIET

HF_DIET

xx<- lm(ALLRAT_2$FA2H~ALLRAT_2$DX*ALLRAT_2$DIET)
anova(xx)

Analysis of Variance Table

Response: ALLRAT_2$FA2H
                          Df  Sum Sq Mean Sq F value    Pr(>F)    
ALLRAT_2$DX                1 0.00004 0.00004  0.0020 0.9649019    
ALLRAT_2$DIET              1 0.33311 0.33311 18.3584 0.0001011 ***
ALLRAT_2$DX:ALLRAT_2$DIET  1 0.08340 0.08340  4.5964 0.0377349 *  
Residuals                 43 0.78023 0.01814                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

shapiro.test(NORMALDIET$CERKL)

    Shapiro-Wilk normality test

data:  NORMALDIET$CERKL
W = 0.9222, p-value = 0.06533

shapiro.test(NORMALDIET$FA2H)

    Shapiro-Wilk normality test

data:  NORMALDIET$FA2H
W = 0.97432, p-value = 0.773

shapiro.test(HF_DIET$CERKL)

    Shapiro-Wilk normality test

data:  HF_DIET$CERKL
W = 0.98217, p-value = 0.9396

shapiro.test(HF_DIET$FA2H)

    Shapiro-Wilk normality test

data:  HF_DIET$FA2H
W = 0.97328, p-value = 0.7668

#library(heatmaply)
#heatmaply(NORMALDIET, main="Rat - Normal Diet", xlab="Genes", ylab="Subjects", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = #c(FALSE, FALSE), hide_colorbar=FALSE, dpi=600)
#heatmaply(HF_DIET, main="Rat - High Fat Diet", xlab="Genes", ylab="Subjects", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = #c(FALSE, FALSE), hide_colorbar=FALSE, dpi=600)

par(mfrow = c(2, 2))

# HUMAN FA2H
#interaction.plot(hpcr_nor$DX,hpcr_nor$SEX,hpcr_nor$FA2H, xlab="DX", ylab="FA2H", main="Human",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , #lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# HUMAN CERKL
#interaction.plot(hpcr_nor$DX,hpcr_nor$SEX,hpcr_nor$CERKL, xlab="DX",  ylab="CERKL", main="Human",  lty=c(1), ylim = c(-1.5,1.5),cex.axis = 0.8, legend=0 ,  col = c("pink", "blue"), #lwd=2.0, pch=c(1,1) ,xpd = F, trace.label = "SEX", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# ALLRAT_2 DIET CERKL
interaction.plot(ALLRAT_2$DX, ALLRAT_2$DIET, ALLRAT_2$CERKL, xlab="DX", ylab="CERKL", main="Rat - All Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 ,legend=0 , col = c("DARK GREEN", "blue") , xpd = F ,lwd=2.0, trace.label = "DIET", dpi=300)
legend("topright", lwd=2.0, legend = c("HF","ND"), lty=c(1), col =  c("DARK  GREEN", "blue"))

#lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "DIET", dpi=300)
# ALLRAT_2 DIET FA2H
interaction.plot(ALLRAT_2$DX, ALLRAT_2$DIET, ALLRAT_2$FA2H, xlab="DX", ylab="FA2H", main="Rat - All Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 ,col = c("DARK  GREEN", "blue") ,xpd = F , lwd=2.0, trace.label = "DIET", dpi=300)
legend("topright", lwd=2.0, legend = c("HF","ND"), lty=c(1), col = c("DARK  GREEN", "blue"))

##interaction.plot(ALLRAT_2$DX, ALLRAT_2$DIET, ALLRAT_2$FA2H, xlab="DX", ylab="FA2H", main="Rat - All Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , ##lwd=2.0,xpd = F , trace.label = "DIET", dpi=300)
##legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))
##interaction.plot(ALLRAT_2$DX, ALLRAT_2$DIET, ALLRAT_2$CERKL, xlab="DX", ylab="FA2H", main="Rat - All Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , ##lwd=2.0,xpd = F , trace.label = "DIET", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# HIGH FAT FA2H



interaction.plot(high_fat$DX, high_fat$SEX, high_fat$FA2H, xlab="DX", ylab="FA2H", main="Rat - High Fat",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0, col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# HIGH FAT CERKL
interaction.plot(high_fat$DX, high_fat$SEX, high_fat$CERKL, xlab="DX", ylab="CERKL", main="Rat - High Fat",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0, col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# HIGH FAT FA2H
#interaction.plot(HF_DIET$DX, HF_DIET$SEX, HF_DIET$FA2H, xlab="DX", ylab="FA2H", main="Rat - High Fat",  l\ty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0, col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# HIGH FAT CERKL
#interaction.plot(HF_DIET$DX, HF_DIET$SEX, HF_DIET$CERKL, xlab="DX", ylab="CERKL", main="Rat - High Fat",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0, col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# NORMAL DIET CERKL
interaction.plot(normal_diet$DX, normal_diet$SEX, normal_diet$CERKL, xlab="DX", ylab="CERKL", main="Rat - Normal Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

#interaction.plot(normal_diet_non$DX, normal_diet_non$SEX, normal_diet_non$CERKL, xlab="DX", ylab="CERKL", main="Rat - Normal Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = #0.8 , legend=0 , col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))


# NORMAL DIET FA2H
interaction.plot(normal_diet$DX, normal_diet$SEX, normal_diet$FA2H, xlab="DX", ylab="FA2H", main="Rat - Normal Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX",dpi=300)
legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# NORMAL DIET CERKL
#interaction.plot(NORMALDIET$DX, NORMALDIET$SEX, NORMALDIET$CERKL, xlab="DX", ylab="CERKL", main="Rat - Normal Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))

# NORMAL DIET FA2H
#interaction.plot(NORMALDIET$DX, NORMALDIET$SEX, NORMALDIET$FA2H, xlab="DX", ylab="FA2H", main="Rat - Normal Diet",  lty=c(1), ylim = c(-1.5,1.5), cex.axis = 0.8 , legend=0 , col = c("pink", "blue") , lwd=2.0,xpd = F , trace.label = "SEX", dpi=300)
#legend("topright", lwd=2.0, legend = c("F","M"), lty=c(1), col = c("pink", "blue"))
       

#hf_nor_2PCR = ALL RAT // NON NORMALIZED
library(dplyr)
ALLRAT <- select(hf_nor_2PCR, -SPECIES, -CHRNA10, -SMYD1)
NUM <- ALLRAT[,4:5]
AR_1 <- fx_z(NUM$CERKL)
AR_2 <- fx_z(NUM$FA2H)
LAB <- ALLRAT[,1:3]
ALLRAT_2 <- data.frame(LAB,AR_1,AR_2)
#hf_2PCR

shapiro.test(AR_2)

    Shapiro-Wilk normality test

data:  AR_2
W = 0.96974, p-value = 0.2589

library(heatmaply)

Loading required package: plotly
Loading required package: ggplot2
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.3.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
You may ask questions at stackoverflow, use the r and heatmaply tags: 
     https://stackoverflow.com/questions/tagged/heatmaply
======================

heatmaply(ALLRAT_2, main="Human", xlab="Genes", ylab="Subjects", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), hide_colorbar=FALSE, dpi=600)

unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
  Reason: image not found

hf_2PCR_1 <-  select(hf_2PCR, -SPECIES, -X., -CHRNA10, -SMYD1)
LAB <-hf_2PCR_1[,1:3]
DAT<-hf_2PCR_1[,4:5]
DAT2 <- fx(DAT)
dietframe <- data.frame(LAB, DAT2)

dietframe

shapiro.test(dietframe$CERKL)

    Shapiro-Wilk normality test

data:  dietframe$CERKL
W = 0.94885, p-value = 0.03903

shapiro.test(dietframe$FA2H)

    Shapiro-Wilk normality test

data:  dietframe$FA2H
W = 0.96974, p-value = 0.2589

heatmaply(ALLRAT, main="Human", xlab="Genes", ylab="Subjects", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), hide_colorbar=TRUE, dpi=600)

normal_diet

shapiro.test(normal_diet$CERKL)

    Shapiro-Wilk normality test

data:  normal_diet$CERKL
W = 0.9222, p-value = 0.06533

shapiro.test(normal_diet$FA2H)

    Shapiro-Wilk normality test

data:  normal_diet$FA2H
W = 0.97432, p-value = 0.773

hfat <- select(high_fat, -DIET, -CHRNA10, -SMYD1)
nfat<-select(normal_diet, -DIET, -CHRNA10, -SMYD1)
             
#hfat <- select(high_fat, -SPECIES, -CHRNA10, -SMYD1)
#hfat
#heatmaply(hfat, main="Rat - High Fat", xlab="Genes", ylab="Subjects", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, #show_dendrogram = c(FALSE, FALSE), hide_colorbar=TRUE, dpi=600)
#heatmaply(nfat, main="Rat - High Fat", xlab="Genes", ylab="Subjects", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, #show_dendrogram = c(FALSE, FALSE), hide_colorbar=TRUE, dpi=600)

NORMALDIET

HF_DIET

library(dplyr)

Warning messages:
1: In readChar(file, size, TRUE) : truncating string with embedded nuls
2: In readChar(file, size, TRUE) : truncating string with embedded nuls
3: In readChar(file, size, TRUE) : truncating string with embedded nuls
4: In readChar(file, size, TRUE) : truncating string with embedded nuls
5: In readChar(file, size, TRUE) : truncating string with embedded nuls
6: In readChar(file, size, TRUE) : truncating string with embedded nuls
7: In readChar(file, size, TRUE) : truncating string with embedded nuls
8: In readChar(file, size, TRUE) : truncating string with embedded nuls
9: In readChar(file, size, TRUE) : truncating string with embedded nuls
10: In readChar(file, size, TRUE) : truncating string with embedded nuls

library(heatmaply)
hpcrnor <- select(hpcr_nor, -SPECIES, -CHRNA10, -SMYD1, -CLIC4, -COL4A1, -FAM189A1, -PTGDR, -SDCCAG8, -TF)
hpcrnor

#S:/SWBB/TTUHSC-Files/Outgoing Tissue_SWBB/Laura O-Dell-UTEP/Publication/FINAL FIGURES/NICOTINE FIGURES R STUDIO
#"E:/R STUDIO/NICOTINE PAPER/CSV NICOTINE/Human.pdf")

heatmaply(hpcrnor, main="Human",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=FALSE, dpi=300, file = "S:/SWBB/TTUHSC-Files/Outgoing Tissue_SWBB/Laura O-Dell-UTEP/Publication/FINAL FIGURES/NICOTINE FIGURES R STUDIO/Human.pdf")

'plotly::orca' is deprecated.
Use 'kaleido' instead.
See help("Deprecated")plotly::orca failed:
 Error: The orca command-line utility is required for this functionality.

Please follow the installation instructions here -- https://github.com/plotly/orca#installation
'plotly::export' is deprecated.
Use 'orca' instead.
See help("Deprecated")'length(x) = 4 > 1' in coercion to 'logical(1)'

#heatmaply(hpcrnor, main="Human",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=TRUE, dpi=300, file = "S:/SWBB/TTUHSC-Files/Outgoing Tissue_SWBB/Laura O-Dell-UTEP/Publication/FINAL FIGURES/NICOTINE FIGURES R STUDIO/Human CB.pdf")

#D:/R STUDIO/    === /Volumes/F4L SWBB/
#webshot::install_phantomjs ()
#library(heatmaply)
#heatmaply(hfat, main="Rat - High Fat",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = #c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=FALSE, dpi=300, file = "D:/R STUDIO/NICOTINE PAPER/CSV NICOTINE/Rat - High Fat.pdf")
#heatmaply(nfat, main="Rat - Normal Diet",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=FALSE, dpi=300, file = "D:/R STUDIO/NICOTINE PAPER/CSV NICOTINE/Rat - Normal Diet.pdf")
#heatmaply(hfat, main="Rat - High Fat",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=TRUE, dpi=300, file = "D:/R STUDIO/NICOTINE PAPER/CSV NICOTINE/Rat - High Fat 2.pdf")
#heatmaply(nfat, main="Rat - Normal Diet",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=TRUE, dpi=300, file = "D:/R STUDIO/NICOTINE PAPER/CSV NICOTINE/Rat - Normal Diet 2.pdf")
#heatmaply(nfat, main="Rat - Normal Diet",  xlab="Genes", col=c("black","red"), row_side_palette= mfcol, labRow = NULL, show_dendrogram = c(FALSE, FALSE), showticklabels = c(T,F), hide_colorbar=TRUE, dpi=300, file = "D:/R STUDIO/NICOTINE PAPER/CSV NICOTINE/Rat - Normal Diet 2.pdf")